Welcome to the X-Cart forums! Please start by reading the forum guidelines (
http://forum.x-cart.com/viewtopic.php?t=6489), and posting your X-Cart version in your signature (click the User CP link at the top of the forum). You can find your version by clicking on the 'Summary' link in your admin area.
As for where to start...well...you need to just dive in to the templates, figure out what is what, and start adding your design to the templates piece by piece. The template guide (which you have probably read) will be very helpful, but there really is no magic bullet to learning the ropes of Smarty or the template structure. Back up your files every time you make a change, or you run the risk of losing hours of work if you botch something up.